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UlthranUlthran
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Merge pull request #52 from PennChopMicrobiomeProgram/48-add-submissions-view-for-each-project-page
Allow bad metadata with warnings and add submissions view on new submission form
2 parents f77a486 + a57afbb commit 44bd599

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7 files changed

+125
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‎.github/workflows/test.yml

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Original file line numberDiff line numberDiff line change
@@ -36,16 +36,8 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.12']
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os: [ubuntu-latest, macos-latest]
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include:
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- python-version: '3.11'
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os: ubuntu-latest
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- python-version: '3.10'
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os: ubuntu-latest
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- python-version: '3.9'
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os: ubuntu-latest
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runs-on: ${{ matrix.os }}
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python-version: ['3.12', '3.11', '3.10', '3.9']
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4

‎README.md

Lines changed: 1 addition & 1 deletion
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@@ -9,7 +9,7 @@ A Flask site for validating metadata sheets per the standards of the PCMP and an
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## Development
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To start with local development:
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This is a Flask app leveraging with bootstrap, jquery, and datatables (via CDN). To start with local development:
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```
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git clone https://github.com/PennChopMicrobiomeProgram/CHOP_metadata_checker.git

‎app/app.py

Lines changed: 32 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,12 @@
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import csv
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import os
3-
from .src.utils import export_table, import_table, run_checks, table_from_file
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from .src.utils import (
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export_table,
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import_table,
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is_importable,
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run_checks,
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table_from_file,
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)
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from .metadatalib.src.metadatalib import SQLALCHEMY_DATABASE_URI
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from .metadatalib.src.metadatalib.consts import ALLOWED_EXTENSIONS
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from .metadatalib.src.metadatalib.models import (
@@ -153,21 +159,18 @@ def download(submission_id):
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return response
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156-
@app.route("/review/<ticket_code>", methods=["GET", "POST"])
157-
def review(ticket_code):
158-
if request.method == "POST":
159-
table_data = session.pop("table_data", {"cols": [], "rows": []})
160-
t = Table(table_data["cols"], table_data["rows"])
161-
import_table(t, db, ticket_code, request.form["comment"])
162-
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return render_template("final.html", ticket_code=ticket_code)
164-
165-
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@app.route("/submit/<ticket_code>", methods=["GET", "POST"])
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def submit(ticket_code):
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project = (
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db.session.query(Project).filter(Project.ticket_code == ticket_code).first()
170166
)
167+
recent_submissions = (
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db.session.query(Submission)
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.filter(Submission.project_id == project.project_id)
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.order_by(Submission.time_submitted.desc())
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.limit(3)
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.all()
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)
171174

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if not project:
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return render_template("dne.html", ticket_code=ticket_code)
@@ -177,6 +180,7 @@ def submit(ticket_code):
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"submit.html",
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filename="Select file ...",
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project=project,
183+
submissions=recent_submissions,
180184
)
181185
elif request.method == "POST":
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# Check if post request has a file
@@ -208,13 +212,30 @@ def submit(ticket_code):
208212
"submit.html",
209213
filename=file_fp.filename,
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project=project,
215+
submissions=recent_submissions,
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table=t,
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checks=checks,
218+
is_importable=is_importable(t),
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)
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return redirect(url_for("submit", ticket_code=project.ticket_code))
216222

217223

224+
@app.route("/review/<ticket_code>", methods=["GET", "POST"])
225+
def review(ticket_code):
226+
if request.method == "POST":
227+
table_data = session.pop("table_data", {"cols": [], "rows": []})
228+
if table_data == {"cols": [], "rows": []}:
229+
flash(
230+
"Something went wrong! There's no metadata in the system to submit. Please try again and be sure not to reload or go back in your browser."
231+
)
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return redirect(url_for("submit", ticket_code=ticket_code))
233+
t = Table(table_data["cols"], table_data["rows"])
234+
import_table(t, db, ticket_code, request.form["comment"])
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236+
return render_template("final.html", ticket_code=ticket_code)
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218239
@app.route("/summary")
219240
def summary():
220241
return render_template(

‎app/src/utils.py

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Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
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from flask_sqlalchemy import SQLAlchemy
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from tablemusthave import Table
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from app.metadatalib.src.metadatalib.consts import (
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CHOP_MANDATORY_TUBE,
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DEFAULT_SAMPLE_FIELDS,
1112
REGEX_TRANSLATE,
1213
)
@@ -99,6 +100,10 @@ def import_table(
99100
return submission
100101

101102

103+
def is_importable(t: Table) -> bool:
104+
return all(col in t.colnames() for col in CHOP_MANDATORY_TUBE)
105+
106+
102107
def export_table(db: SQLAlchemy, submission_id: int) -> Table:
103108
samples = (
104109
db.session.query(Sample).filter(Sample.submission_id == submission_id).all()

‎app/templates/index.html

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Original file line numberDiff line numberDiff line change
@@ -19,4 +19,13 @@ <h5 class="m-3">Please submit your project id below to get to the metadata submi
1919
<button type="submit" class="btn btn-success m-3">GO</button>
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</form>
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</div>
22+
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<div class="p-4">
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<h3> Welcome to the CHOP Microbiome Metadata Checker! </h3>
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<p class="w-50">This website is used to validate your metadata spreadsheet used in bioinformatics analyses for the PennCHOP Microbiome Center. It will parse your spreadsheet to ensure it fulfills certain specifications and display error messages for columns and cells that do not meet these specifications.</p>
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<p class="w-50">To get started, enter your project code above or go directly to the URL you were received. Once there, you can Upload Metadata (csv, tsv, or txt files only; if you have an Excel sheet you'll have to export it to one of these formats) and the checker will determine if there are any issues. If there are none, you can Submit Metadata, provide an optional comment, and then you'll be done! If there are issues but they won't break anything immediately, you can proceed but with caution. If there are breaking issues, you will have to fix them and reupload your metadata.</p>
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<p class="w-50">To view previous submissions for your project, enter your project code and Go. On the metadata submission page you will see a list of your most recent submissions.</p>
30+
</div>
2231
{% endblock %}

‎app/templates/project.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,9 @@ <h3 class="m-3">{{project.contact_name}} :-: {{project.contact_email}}</h3>
2525
</tr>
2626
{% endfor %}
2727
</tbody>
28-
</table>
28+
</table>
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30-
<script type="text/javascript">
30+
<script type="text/javascript">
3131
$(document).ready(function () {
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/* Initialize the DataTable */
3333
oTable = $('#submissions').dataTable({
@@ -49,5 +49,5 @@ <h3 class="m-3">{{project.contact_name}} :-: {{project.contact_email}}</h3>
4949
/* Redraw manually */
5050
oTable.fnDraw();
5151
});
52-
</script>
52+
</script>
5353
{% endblock %}

‎app/templates/submit.html

Lines changed: 73 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -1,38 +1,89 @@
11
{% extends 'base.html' %}
22
{% import 'macros.jinja' as macros %}
33

4-
{% block head %}
5-
{% endblock %}
6-
74
{% block body %}
85

96
<body>
10-
<div class="card m-3">
11-
<h2 class="m-3">{{project.project_name}}</h2>
12-
<h3 class="m-3">{{project.contact_name}} :-: {{project.contact_email}}</h3>
13-
<div class="card-body">
14-
<form action="{{ '/submit/' + project.ticket_code }}" method="POST" enctype="multipart/form-data">
15-
<div class="form-group">
16-
<label>Select metadata file</label>
17-
<div class="row">
18-
<div class="col-sm">
19-
<div class="custom-file">
7+
<div class="flex card m-3">
8+
<div class="container-fluid p-4 card-body">
9+
<div class="row">
10+
<div class="col-lg">
11+
<h2 class="m-3">{{project.project_name}}</h2>
12+
<h3 class="m-3">{{project.contact_name}} :-: {{project.contact_email}}</h3>
13+
<form action="{{ '/submit/' + project.ticket_code }}" method="POST" enctype="multipart/form-data">
14+
<div class="form-group">
15+
<label>Select metadata file</label>
16+
<div class="custom-file py-2">
2017
<input type="file" class="custom-file-input" name="metadata_upload" id="metadata_upload">
2118
<label class="custom-file-label" for="metadata_upload" id="filename">{{ filename }}</label>
2219
</div>
20+
<button type="submit" class="btn btn-success">Upload Metadata</button>
2321
</div>
24-
<div class="col-sm">
25-
<button type="submit" class="btn btn-success">Upload metadata</button>
26-
</div>
22+
</form>
23+
24+
<div class="py-4">
25+
{% if checks is defined %}
26+
{% if checks['passed'] %}
27+
<a href="{{ url_for('review', ticket_code=project.ticket_code) }}" class="btn btn-success">Submit Metadata</a>
28+
{% elif is_importable %}
29+
<a href="{{ url_for('review', ticket_code=project.ticket_code) }}" class="btn btn-warning" onclick="return confirm('There are still issues in your metadata. Are you sure you want to submit with these issues?')">Submit Metadata</a>
30+
<i class="max-w-prose">There are still issues flagged by the checker but you can submit if you want.</i>
31+
{% else %}
32+
<i class="max-w-prose">There are schema-breaking issues flagged by the checker. You must resolve these issues before you can submit.</i>
33+
{% endif %}
34+
{% endif %}
2735
</div>
2836
</div>
29-
</form>
30-
31-
{% if checks is defined %}
32-
{% if checks['passed'] %}
33-
<a href="{{ url_for('review', ticket_code=project.ticket_code) }}" class="btn btn-success">Submit Metadata</a>
34-
{% endif %}
3537

38+
<div class="col-md">
39+
<h4>Recent Submissions</h4>
40+
<table class="display" id="submissions">
41+
<thead>
42+
<tr>
43+
<th>Submission ID</th>
44+
<th>Version</th>
45+
<th>Time Submitted</th>
46+
<th>Comment</th>
47+
</tr>
48+
</thead>
49+
<tbody>
50+
{% for submission in submissions %}
51+
<tr>
52+
<td><a href="{{ url_for('show_submission', submission_id=submission.submission_id) }}">{{ submission.submission_id }}</a></td>
53+
<td>{{ submission.version }}</td>
54+
<td>{{ submission.time_submitted }}</td>
55+
<td>{{ submission.comment }}</td>
56+
</tr>
57+
{% endfor %}
58+
</tbody>
59+
</table>
60+
61+
<script type="text/javascript">
62+
$(document).ready(function () {
63+
/* Initialize the DataTable without the search bar and pagination */
64+
oTable = $('#submissions').dataTable({
65+
"bSort": false,
66+
"iDisplayLength": 20,
67+
"bLengthChange": false,
68+
"bPaginate": false, // Disable pagination
69+
"bStateSave": true,
70+
"bFilter": false, // Disable the search bar
71+
});
72+
73+
/* Snap pagination info to grid */
74+
$("#submissions_info").addClass("span-12");
75+
76+
/* Redraw manually */
77+
oTable.fnDraw();
78+
});
79+
</script>
80+
</div>
81+
</div>
82+
</div>
83+
</div>
84+
85+
<div>
86+
{% if checks is defined and table is defined %}
3687
{{ macros.table(table, checks) }}
3788
{% endif %}
3889
</div>

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